3pgk: Difference between revisions

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 ==The structure of yeast phosphoglycerate kinase at 0.25 nm resolution==
-<StructureSection load='3pgk' size='340' side='right' caption='[[3pgk]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+<StructureSection load='3pgk' size='340' side='right'caption='[[3pgk]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3pgk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1pgk 1pgk]. The February 2004 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''The Glycolytic Enzymes''  by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2004_2 10.2210/rcsb_pdb/mom_2004_2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PGK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PGK FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3pgk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1pgk 1pgk]. The February 2004 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''The Glycolytic Enzymes''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2004_2 10.2210/rcsb_pdb/mom_2004_2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PGK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PGK FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3PG:3-PHOSPHOGLYCERIC+ACID'>3PG</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3PG:3-PHOSPHOGLYCERIC+ACID'>3PG</scene>, <scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoglycerate_kinase Phosphoglycerate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.2.3 2.7.2.3] </span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3pgk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pgk OCA], [https://pdbe.org/3pgk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pgk RCSB], [https://www.ebi.ac.uk/pdbsum/3pgk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pgk ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3pgk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pgk OCA], [http://pdbe.org/3pgk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3pgk RCSB], [http://www.ebi.ac.uk/pdbsum/3pgk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3pgk ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/PGK_YEAST PGK_YEAST]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
    <jmolCheckbox>
-     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pg/3pgk_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pg/3pgk_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 19: / Line 20: @@
 </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3pgk ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The structure of yeast phosphoglycerate kinase has been determined with data obtained from amino acid sequence, nucleotide sequence, and X-ray crystallographic studies. The substrate binding sites, as deduced from electron density maps, are compatible with known substrate specificity and the stereochemical requirements for the enzymic reaction. A carboxyl-imidazole interaction appears to be involved in controlling the transition between the open and closed forms of the enzyme.
-Sequence and structure of yeast phosphoglycerate kinase.,Watson HC, Walker NP, Shaw PJ, Bryant TN, Wendell PL, Fothergill LA, Perkins RE, Conroy SC, Dobson MJ, Tuite MF, et al. EMBO J. 1982;1(12):1635-40. PMID:6765200<ref>PMID:6765200</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3pgk" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Phosphoglycerate Kinase|Phosphoglycerate Kinase]]
+*[[Phosphoglycerate kinase 3D structures|Phosphoglycerate kinase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Atcc 18824]]
+[[Category: Large Structures]]
-[[Category: Phosphoglycerate kinase]]
 [[Category: RCSB PDB Molecule of the Month]]
+[[Category: Saccharomyces cerevisiae]]
 [[Category: The Glycolytic Enzymes]]
-[[Category: Shaw, P J]]
+[[Category: Shaw PJ]]
-[[Category: Walker, N P]]
+[[Category: Walker NP]]
-[[Category: Watson, H C]]
+[[Category: Watson HC]]
-[[Category: Transferase]]